7KF3

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

• PDB DOI: https://doi.org/10.2210/pdb7KF3/pdb

• Classification: LYASE
• Organism(s): Brucella abortus 2308
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2020-10-13 Released: 2020-11-04 
• Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.210 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 

Starting Model: experimental

Literature

Crystal structure of GDP-mannose 4,6-dehydratase from Brucella abortus (strain 2308) in complex with Guanosine-diphosphate-rhamnose

Abendroth, J., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.

To be published.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 173.34 kDa 
• Atom Count: 12,289 
• Modelled Residue Count: 1,448 
• Deposited Residue Count: 1,476 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-mannose 4,6-dehydratase	A, B, C, D	369	Brucella abortus 2308	Mutation(s): 0  Gene Names: gmd, BAB1_0545 EC: 4.2.1.47
UniProt
Find proteins for Q2YMP3 (Brucella abortus (strain 2308)) Explore Q2YMP3  Go to UniProtKB:  Q2YMP3

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAP (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H28 N7 O17 P3 XJLXINKUBYWONI-NNYOXOHSSA-N
GDR (Subject of Investigation/LOI)	E [auth A], G [auth B], I [auth C], K [auth D]	GUANOSINE-5'-DIPHOSPHATE-RHAMNOSE C16 H25 N5 O15 P2 LQEBEXMHBLQMDB-GDJBGNAASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 0.210 
• R-Value Work: 0.174 
• R-Value Observed: 0.175 
• Space Group: P 1
• Diffraction Data: https://doi.org/10.18430/m37kf3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.13	α = 89.06
b = 93.3	β = 78.91
c = 93.77	γ = 87.51

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
PHENIX	model building
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description